I have to check over my paragraph indents every time I go into my LibreOffice document even after saving the mss. Anyone have that problem?
The mms is @ 350 pages. Is that the problem?
Your indents are part of the paragraph style and will be consistent, unless you are direct formatting them and making a huge amount of unnecessary extra work for yourself.
I suggest reading about styles in chapter nine of the Writer Guide 6.4
If you have applied direct formatting a lot (that is formatting from the toolbar buttons), that may cause this problem. Size isn’t the problem. But if you want consistent formatting in a document that size, you really need to learn about styles. They are indispensable.
Read these guidelines and ask a good question. Write in plain English. In particular, do not use obscure acronyms: what is/are mms/mss?
I assumed ms to be manuscript, I ignored the extra letters as they seemed to be mere ornamentation. Al
According to Wikipedia, MMS is short for the plural of manuscript. So, what’s the problem? Please stop trolling and try to be helpful. 
The question appears to refer to a single manuscript so I’m sticking with ornamentation
Probably the best thing is play around with a copy of the original. I am assuming for this that direct formatting has been applied throughout but inconsistently, and the underlying styles are what you would see if you created a new document from LibreOffice. It also assumes you have used Heading styles for headings, not just a change in size, font, boldness, although they might survive even so.
We should modify the Text Body style (the next style after a heading) to give the indent (and line spacing, if that is an issue too) that we want. Open the styles sidebar (F11) and make sure the leftmost icon, paragraph styles is selected.
Right-click on Text Body and select Modify… In the dialog that opens select the tab labelled Indents & Spacing, define your indents, line spacing and spacing to next paragraph. OK out, some of your paragraphs might already change to reflect the new settings but ignore that for the moment.
Changing to another paragraph style will remove some of the direct formatting, in particular indents, line spacing, and paragraph spacing. Press Ctrl+H to bring up the Find and Replace dialog. Tick the box that says Paragraph Styles, in Find drop-down select Text Body , in the Replace select one nearby that you haven’t used for anything, say Text Body Indent. Click Replace All.
Now in the Find dialog select Text Body Indent, then in the Replace select Text Body, click Replace All. This will have removed any direct formatting relating to indents, line and paragraph spacing and applied the default. Hopefully, it will have left all the other direct formatting such as Bold, Italic, etc.
As some text could be also Default Style, it might be worth Find, Default Style and Replace with Text Body.
To see what styles you have in your document, you can click on the drop-down box at the bottom of the Styles sidebar and select Applied styles.
I haven’t done this except on a few pages as a test. I don’t know anything about the construct of your document, the styles, formatting, additions, etc. so try on a copy of your ms and let us know if it works for you. Cheers, Al
Afterthought: to change the indent in future, you just have to right-click the Text Body Style and select Modify… One change will update all of that style (if not over-ridden by direct formatting)