Quirke faced charges of burglary and having a key to Lowry's home
Patrick Quirke was charged in 2012 with two burglaries and with possession of a key to Mary Lowry's house - however, the DPP directed the charges be dropped.
A senior garda gave evidence about the charges during the trial of Patrick Quirke (50), with an address at Breanshamore, Co Tipperary.
Mr Quirke has pleaded not guilty to the murder of Bobby Ryan (52), a part-time DJ known as 'Mr Moonlight', on a date between June 3rd, 2011, and April 2013.
Chief Superintendent Dominic Hayes agreed under cross-examination that prior to 2011, Mr Quirke had no previous convictions or criminal history.
He also agreed that "various difficulties" arose between Mary Lowry and Mr Quirke between 2011 and 2013 which resulted in him being charged with two burglaries and possession of the key to her house.
The trial has previously heard evidence Mr Quirke had an affair with Ms Lowry - the sister-in-law of his wife Imelda Quirke - between January 2008 and 2010 after the death of Ms Lowry's husband.
Ms Lowry ended the relationship with Mr Quirke, meeting Mr Ryan soon after and began a relationship with him which she says continued until his death.
Chief Supt Hayes told the gardaí charged Mr Quirke in relation to the two burglaries and the matter came before the courts. However, the DPP directed the charges be dropped.
The body of Mr Ryan was found in a run-off tank on Ms Lowry's farm in April 2013.
Speaking about the process of the removal of Mr Ryan's remains from the tank, Chief Supt Hayes said he was "very sure" there were no injuries inflicted on the body from falling debris when the concrete slab of the tank broke - though he conceded his right arm had subsequently become detached.
He told the court that he was present when the digger was put in place, in preparation for the lid being lifted, and had removed as much as he could of the clay that was covering the tank.
"Whilst some very minor debris did fall in on the tank, no large piece of debris or concrete fell on Mr Ryan," he said.
Asked why he did not mention this in his statement, he said it was not possible for him to make a statement regarding questions or issues that may arise.
Lorcan Staines SC, for the defence, put it to him that Professor Jack Crane, the former State pathologist of Northern Ireland, had said that he could not exclude the possibility of the fracture of Mr Ryan's leg occurring if a large heavy piece of concrete fell on his remains.
However, Chief Supt Hayes said: "No, it certainly wasn't caused by any debris falling in the removal."
On another issued, it was put to Chief Supt Hayes by Mr Staines that there was a "systems failure" which led to fingerprints from Bobby Ryan's van and from items found in it in 2011 not being tested until this year.
Mr Staines said prints taken from the van were not checked against those of the accused until January 2019, while prints from the items - a diary and driver's licence - were not tested until last Thursday.
Chief Supt Hayes said the fingerprints should have been tested before then.
He said if so-called "elimination prints" were sent to Garda Headquarters, he would have expected them to be tested before this year.
Chief Supt Hayes earlier told Michael Bowman SC, for the prosecution, that he observed the body of Bobby Ryan lying "in what appeared to be sludge" and was satisfied that a health and safety risk was present. When the fire brigade arrived at the scene, gardai sought their expertise in removing the body from the tank.
Asked how the body appeared physically, Chief Supt Hayes said it was very badly decomposed and lying face down.
"From my observation of both the body in the tank and when it was removed, it was not apparent to me that it was naked," he said.
Mr Staines put it to Chief Supt Hayes that Dr Michael Curtis described the breaking of the slab as "important information" which he ought to have known about.
However, Chief Supt Hayes said he did not believe it was important "in the overall scheme".
He subsequently added that Dr Curtis was provided with a "full album of photographs" which showed "very clearly" that the lid broke.
Mr Staines asked if gardaí had been "badly let down" by then deputy State pathologist Dr Khalid Jaber, who did not go to the scene despite being requested.
However, Chief Supt Hayes said it had no negative impact and the best person to assist in removing the body was Detective Garda John Grant of the Technical Bureau, who advised throughout the process.
Meanwhile under cross-examination, he agreed that the Heritage hotel in Portlaoise had confirmed thatPatrick Quirke and his wife Imelda had stayed there on June 3 and 4, 2011, for Imelda's birthday at a cost of €641. The package was booked on May 8, 2011.
Phone records suggested Mr Quirke's phone pinged off masts in Portlaoise from 13.56pm on June 3, 2011, continuing until 16.50pm on June 5, 2011.
The trial continues.